Ligand profile

EDG

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_2724 — beta-xylosidase

Via homolog PDB 5jox UniProt A7LXT8 Formula C₅H₁₁NO₃
Mol. weight 133.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EDG
PDB
5jox
UniProt (similar protein)
A7LXT8
Target protein
VK055_2724

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 133.15 Da
LogP (Crippen) -2.33
H-bond donors 4
H-bond acceptors 4
TPSA 72.72 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 9
Fraction sp³ C 1.00
Formula C₅H₁₁NO₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 72.7
  • −1 ≤ LogP ≤ 5 -2.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 133.1
  • LogP ≤ 5 -2.33
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 72.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H](N1)CO)O)O
InChI 
InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4-,5-/m0/s1
InChIKey 
OQEBIHBLFRADNM-YUPRTTJUSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF04616

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2724.

PDB 3

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)